I'm having a very hard time making R CMD check produce a clean check on
examples because of the timings inserted into examples by R CMD check.
I am getting a difference on every example output caused by timing
information being inserted by 'R CMD check'.
The current 'Writing R Extensions' manual[1] states on p. 14:
If directory tests has a subdirectory Examples containing a
file pkg-Ex.Rout.save, this is compared to the output file
for running the examples when the latter are checked.
Reference output should be produced without having the
--timings option set (and note that --as-cran sets it).
As is suggested above, if I run
R CMD check --as-cran mypkg.tar.gz
or
R CMD check --timings mypkg.tar.gz
the my.pkg.Rcheck/mypkg-Ex.Rout file contains timing lines inserted by
'R CMD check'
If, instead, I follow my reading of the manual, and run
R CMD check mypkg.tar.gz
the mypkg.Rcheck/mypkg-Ex.Rout file does not contain timings. If I then
copy the mypkg.Rcheck/mypkg-Ex.Rout file to
mypkg/tests/Examples/mypkg-Ex.Rout.save
as described by footnote 17 on the previously referenced p. 14, I would
expect to now have no differences, as demonstrated by 'diff' or 'diff
-bw' as used by 'R CMD check'.
To my surprise, whether I copy a version of the mypkg-Ex.Rout file with
or without timing rows, I get differences reported for every example by
the (spurious?) insertion of timings by R CMD check.
e.g.
8169a8549,8550
> > base::assign(".dptime", (proc.time() - get(".ptime", pos =
"CheckExEnv")), pos = "CheckExEnv")
> > base::cat("textplot", base::get(".format_ptime", pos =
'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n",
file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
8175a8557
Is this expected?
It is certainly not the behavior we had for many years, where a check of
examples could actually be clean, producing differences only on the
'Time elapsed:' line, which has been present for many R versions. I
have tried testing against a package with both the timing lines includes
and excluded in /mypkg-Ex.Rout.save, and with R CMD check run without
additional options, with --timings, and with --as-cran. They produce
equivalent check files. on their example checks.
This behavior is on R 3.1.0, 3.1.1, and R-devel.
I would assume from the documentation that there should be a way to get
a clean check, without the timing diffs.
Advice appreciated,
Brian
Ref:
[1] http://cran.r-project.org/doc/manuals/R-exts.pdf
--
Brian G. Peterson
http://braverock.com/brian/
Ph: 773-459-4973
IM: bgpbraverock
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